(first question, hi!) At the moment, I am trying to bring a planet which contains an atmosphere that can barely be breathed by humans (14% oxygen to be precise), to life. This planet is abundant with lush ecosystems of (mainly) turquoise and blue flora and fauna, and orbits the Goldilocks zone of an orange dwarf 0.8 times the size of our Sun. What could make up the other 86% of the atmosphere? and how would it affect a human's perception of the color of the sky?
Maybe the same stuff we have on Earth?
Imagine 100 people at a concert. 14 are from Iowa. That crowd is 14% Iowans and it is ok because they are into it. Then the van from Council Bluffs shows up just in time for the main act with 14 more Iowans. Now the crowd of 114 with 28 Iowans is 24% Iowans. Higher % of Iowans and also a bigger crowd.
So too oxygen. Atmosphere is not an absolute number. You can get more of it, or you can lose it to chemistry or to space. If you don't want to get too creative just have it be what we have now: mostly nitrogen, a squidge of CO2, some argon. Lower % O2 and less total atmosphere.
Or have a bucketload of CO2.
You want a green world where it is hard to breathe? Add a bunch of CO2. The ancient atmosphere might have had a lot of CO2 - maybe as much as 70%. That would make it tough to breathe normally because CO2 is what triggers our breathing,. Everyone would be hyperventilating like mad and feel like they were suffocating, oxygen notwithstanding. Also the CO2 dissolves into body water and makes it acidic.
But the plants dig it. Plants need CO2 to make their bodies and everything else. When there is a lot, they can keep pores closed more and they lose less water. A high CO2 world could be (and maybe was!) a very happy plant world.
Lots of plants can readily withstand a moderate amount of atmospheric hydrogen cyanide. Some even produce the stuff, albeit as a non-volatile glycoside.
But humans... not so much. Most other species with red blood also don't fare so well. You need to be noble, have the bluest of blue blood... in that you don't want an iron-based oxygen mediation molecule, and copper-based (like the horseshoe crab or Spock) is typically blue.
You needn't have too much hydrogen cyanide in circulation, just enough to exceed the LD50 by means of skin absorption.
The main constituent of the remainder of the atmosphere is likely to be nitrogen. There's apparently oxygen-producing photosynthetic plants which would have consumed most of the CO2 by the time there were "lush ecosystems" on land, most of the CO2 the atmosphere started with was probably the source of the O2 it has now. There aren't many other options that are both stable in an oxygen-rich atmosphere and likely to be found in quantities large enough to produce an atmosphere. Additionally, nitrogen is necessary for protein chemistry, and unlike CO2 it is unreactive enough that it's unlikely for life to have consumed most of it.
Trace gases can still render the atmosphere unsuitable for humans. Another answer mentions hydrogen cyanide, other options are hydrogen sulfide and carbon monoxide, or even formaldehyde. HCN, HS, and CO are all lethal at levels of a couple hundred ppm. Formaldehyde, CH2O, is irritating to the eyes and respiratory tract at a fraction of a ppm and can cause sensitization with allergic reactions on later exposure, and long term exposure to low levels can cause nervous system damage and increase risk of cancer. It's also quite easy to produce biologically. Or the local plant life could fill the atmosphere with pollen and spores that cause allergic reactions.
The trace gases wouldn't have any visible effect. Pollen/spores can be visible in high densities, and could cause redder sunrises/sunsets at lower concentrations.